Genomic targeting and high-resolution mapping of the domestication gene Q in wheat

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 706-718 ◽  
Author(s):  
Justin D Faris ◽  
Bikram S Gill
Keyword(s):  
Positional Cloning ◽  
Agronomic Traits ◽  
Physical Map ◽  
Regulatory Gene ◽  
Fold Increase ◽  
Substitution Lines ◽  
Deletion Lines ◽  
Density Mapping ◽  
Chromosome 5A ◽  
Q Gene

The Q locus is largely responsible for the domestication of bread wheat. Q confers the free-threshing character of the spike and influences other important agronomic traits. Using chromosome deletion lines, Q was placed on the physical map within a submicroscopic segment of the long arm of chromosome 5A. We targeted markers to the segment by comparative mapping of anonymous RFLP clones, AFLP, and mRNA differential display analysis of deletion lines 5AL-7 and -23, which have deletion breakpoints that flank the Q locus. Differentially expressed sequences detected fragments at various loci on group 5 chromosomes suggesting that Q may be a regulatory gene. We identified 18 markers within the Q gene deletion interval and used them to construct a genetic linkage map of the region in F2 populations derived from chromosome 5A disomic substitution lines. The genetic map corresponding to the deletion segment was 20-cM long, and we identified markers as close as 0.7 cM to the Q gene. An estimate of base pairs per centimorgan within the region is 250 kb/cM, an 18-fold increase in recombination compared with the genomic average. Genomic targeting and high-density mapping provide a basis for the map-based cloning of the Q gene.Key words: Triticum aestivum, positional cloning, physical mapping.

scholarly journals Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

2020 ◽  
Author(s):  
De Zhu ◽  
Ximei Li ◽  
Zhiwei Wang ◽  
Chunyuan You ◽  
Xinhui Nie ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Genetic Improvement ◽  
Agronomic Traits ◽  
Physical Map ◽  
Leaf Shape ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Substitution Lines ◽  
Multiple Alleles

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization.Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

scholarly journals Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 823-835 ◽  
Author(s):  
Justin D Faris ◽  
Karri M Haen ◽  
Bikram S Gill
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Hot Spot ◽  
Chromosome Breakage ◽  
Small Chromosome ◽  
Gene Density ◽  
Chromosome 5B ◽  
High Gene ◽  
The Many ◽  
Recombination Hot Spots

AbstractPhysical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.

scholarly journals A4Mb High Resolution BAC Contig on Bovine Chromosome1q12and Comparative Analysis With Human Chromosome21q22

2005 ◽  
Vol 6 (4) ◽  
pp. 194-203 ◽  
Author(s):  
Cord Drögemüller ◽  
Anne Wöhlke ◽  
Tosso Leeb ◽  
Ottmar Distl
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Dominant Gene ◽  
Bac Library ◽  
Exact Order ◽  
Bac Contig ◽  
Nucleotide Sequence Data ◽  
New Genes ◽  
Human Genes ◽  
First Time

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genesKRTAP8P1andCLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed thein silicomapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine–human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle. The nucleotide sequence data reported in this paper have been submitted to EMBL and have been assigned Accession Numbers AJ698510–AJ698674.

scholarly journals Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

2020 ◽  
Author(s):  
De Zhu ◽  
Ximei Li ◽  
Zhiwei Wang ◽  
Chunyuan You ◽  
Xinhui Nie ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Genetic Improvement ◽  
Oil Content ◽  
Agronomic Traits ◽  
Physical Map ◽  
Leaf Shape ◽  
Cottonseed Oil ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Multiple Alleles

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTLs) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Genetic and contig map of a 2200-kb region encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1086-1092 ◽  
Author(s):  
Christian S. Hardtke ◽  
Thomas Berleth
Keyword(s):  
Arabidopsis Thaliana ◽  
Positional Cloning ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Primary Root ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Caps Markers ◽  
Yac Contig

In the course of the isolation of the MONOPTEROS (MP) gene, required for primary root formation in Arabidopsis thaliana, a yeast artificial chromosome (YAC) contig encompassing approximately 2200 kilobases corresponding to 5.5 cM on the top arm of chromosome 1 was established. Forty-six YAC clones were characterized and 12 new restriction fragment length polymorphism (RFLP) markers are presented. Three new codominant amplified polymorphic sequence (CAPS) markers were generated that enabled high resolution genetic mapping and correlation of physical and genetic distances along the contig. The map contributes to the completion of a physical map of the Arabidopsis genome and should facilitate positional cloning of other genes in the region as well as studies on genome organization. We also present another set of 11 physically linked probes, as well as mapping data for additional RFLP markers within a broader interval of 10.4 cM. Key words : Arabidopsis, CAPS markers, MONOPTEROS gene, physical map, RFLP markers, YAC contig.

Analysis of proteome and frost tolerance in chromosome 5A and 5B reciprocal substitution lines between two winter wheats during long-term cold acclimation

PROTEOMICS ◽  
2011 ◽  
Vol 12 (1) ◽  
pp. 68-85 ◽  
Author(s):  
Pavel Vítámvás ◽  
Ilja T. Prášil ◽  
Klára Kosová ◽  
Sébastien Planchon ◽  
Jenny Renaut
Keyword(s):  
Cold Acclimation ◽  
Frost Tolerance ◽  
Substitution Lines ◽  
Chromosome 5A

scholarly journals Over-expression of the brassinosteroid gene TaDWF4 increases wheat productivity under low and sufficient nitrogen through enhanced carbon assimilation

2021 ◽  
Author(s):  
Matthew John Milner ◽  
Stéphanie M. Swarbreck ◽  
Melanie Craze ◽  
Sarah Bowden ◽  
Howard Griffiths ◽  
...  
Keyword(s):  
Crop Yields ◽  
Agronomic Traits ◽  
Carbon Assimilation ◽  
Fold Increase ◽  
Operating Efficiency ◽  
Over Expression ◽  
Rate Limiting Step ◽  
Marginal Soils ◽  
Use Efficiency ◽  
Rate Limiting

There is a strong pressure to reduce nitrogen (N) fertiliser inputs while maintaining or increasing current cereal crop yields. Brassinosteroids, (BR), are a group of phytohormones essential for plant growth and development, that have been demonstrated to regulate several agronomic traits. DWF4 encodes a cytochrome P450 that catalyses a rate-limiting step in BR synthesis. We show that overexpression of the dominant shoot expressed homoeologue TaDWF4-B in wheat can increase plant productivity by up to 105% under a range of N levels on marginal soils, resulting in increased N use efficiency (NUE). We show that a two to four-fold increase in TaDWF4 transcript levels enhances the responsiveness of genes regulated by N. The productivity increases seen were primarily due to the maintenance of photosystem II operating efficiency and carbon assimilation in plants when grown under limiting N conditions and not an overall increase in photosynthesis capacity. The increased biomass production and yield per plant in TaDWF4 OE lines could be linked to modified carbon partitioning and changes in expression pattern of the growth regulator Target Of Rapamycin, offering a route towards breeding for sustained yield and lower N inputs.

scholarly journals Development of a sequence-based reference physical map of pea (Pisum sativum L.)

2019 ◽  
Author(s):  
Krishna Kishore Gali ◽  
Bunyamin Tar’an ◽  
Mohammed-Amin Madoui ◽  
Edwin van der Vossen ◽  
Jan van Oeveren ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Physical Map ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Bac Clones ◽  
Pooled Dna ◽  
Mapping Technology ◽  
Generation Sequencing

AbstractWhole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

scholarly journals Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience ◽  
2020 ◽  
Vol 9 (9) ◽  
Author(s):  
Gina M Pham ◽  
John P Hamilton ◽  
Joshua C Wood ◽  
Joseph T Burke ◽  
Hainan Zhao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Agronomic Traits ◽  
Solanum Tuberosum L ◽  
Fold Increase ◽  
High Quality ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

Abstract Background Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. Findings Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

Sign in / Sign up

Export Citation Format

Share Document